Michael Macias

`squab quantify` produces [htseq-count](https://htseq.readthedocs.io/en/latest/htseqcount.html)-compatible output. I suspect it should already be picked up by the [htseq module](https://docs.seqera.io/multiqc/modules/htseq), given the regex in the file search pattern. squab can ultimately be treated...

The error message is printing the invalid character in hex, though there's a slight issue with the formatting. `0x67` is `g`. Complementing lowercase bases was recently added to noodles 0.75.0/noodles-fasta...

Should this be further constrained to unmapped records with _missing_ mapping qualities? That is, recommend using 0 instead of 255. Otherwise, is this recommending that all unmapped records have their...

As an extra datapoint, htsjdk 4.1.3 rejects unmapped records with a mapping quality > 0. ```console $ java -jar picard.jar ViewSam --INPUT in.sam --ALIGNMENT_STATUS All --PF_STATUS All [...] [Fri Jan...

I'm referring to the _Code_ column of the standard common types table under the `MM` description. It defines codes that are uppercased, but the `MM` field pattern does not allow...

> If this is something you think would be reasonably straightforward I would be willing to draft a PR with some guidance on where to start. Yes, give it a...

> I wonder if it also makes sense to add an asynchronous version of an indexed reader? Tracked in #296.

> ``` > = note: expected struct `noodles_cram::Record` > found reference `&dyn noodles_sam::alignment::Record` > ``` > > Is that a change that should be made in a separate PR? For...

The alternative is to link to [libdeflate](https://github.com/ebiggers/libdeflate), which can be done by adding noodles-bgzf to your project with the `libdeflate` feature enabled. ```console $ cargo add noodles-bgzf --features libdeflate ```...

hdf5-sys seems to statically link to stock zlib. I'm unsure how flate2 could be affecting it. There is no trivial way to revert back to the default flate2 backend miniz_oxide...